Below are example templates generated for demo trial data from a 2020 workshop.
You can use these files to see how the templates are properly formatted.
All data (such as Accessions and Trials) are associated with a particular Breeding Program. Generally,
we have a Breeding Program for each University / Institution that submits data to the database. For
cooperative / nursery trials, there may be a Breeding Program created specifically for the nursery
(ex: Uniform Oat Performace Nursery). Trials performed for the nursery are associated with the nursery
Breeding Program in order to keep them grouped together in the database.
Make sure your Breeding Program exists in the Database
Each Trial needs to be associated with a single Location and the Location needs to exist in the database before adding a Trial.
Most of our trials are associated with a location of the closest town to the field site. However, more specific locations can be used
(such as a separate location for each field).
Check the table below to see if the Location(s) of your Trial(s) have already been created.
A phenotyping trial must be linked to a specific location. Generally, the location of a trial is set as the
closest town to the actual field site. However, more specific locations can be added (such as separate locations
for each farm and/or field).
T3/Wheat uses the following naming conventions for the Location name and abbreviation:
Type of Location
Name Convention
Name Example
Abbreviation Convention
Abbreviation Example
Location Type
Town (closest to field site)
{Town name}, {2-letter State / Province abbreviation}
Ithaca, NY
{First 3 letters of town name}{2-letter State / Province abbreviation}
ITHNY
Town
Farm (a specific farm site, but an unknown / unspecified field at the farm)
{Town name}, {2-letter State / Province abbreviation} - {Farm name}
Ithaca, NY - Caldwell
{First 3 letters of town name}{2-letter State / Province abbreviation}-{First 3 letters of the Farm name}
ITHNY-CAL
Farm
Field (a specific field within a farm site)
{Town name}, {2-letter State / Province abbreviation} - {Farm name} - {Field identifier}
Ithaca, NY - Caldwell - A
{First 3 letters of town name}{2-letter State / Province abbreviation}-{First 3 letters of Field name}-{Field ID}
ITHNY-CAL-A
Field
These are suggested naming conventions, but can be changed if there are conflicts with existing locations
or a different abbreviation is more suitable for a specific Location.
Make sure the Location of your Trial(s) exist in the Database
Make sure your Breeding Program is associated with the location.
In the Location Table on the Manage > Locations page, the Program
column lists all of the Breeding Programs associated with each Location.
If your Breeding Program is NOT associated with the Location:
Find the location on the map
Click the Edit link
In the Program select box, ctrl-click / command-click
your Breeding Program from the list to add it to the existing Breeding Programs already associated with the location.
Click the Store Location Details button to save your changes.
Accessions
The contents of each plot must be associated with a single Accession (germplasm line). The Accession
must exist in the database before a Trial can be created. Also, you must refer to the exact spelling and letter-case of
the Accession's name (or synonym) in the database when creating the Trial.
We try very hard to avoid creating duplicate entries of an Accession based on variations in the spelling
and/or characters used in the Accession name. Therefore, whenever you upload an accession or trial template, all of the
accession names in the file are automatically sent to the BrAPI Germplasm Search Tool
to find any existing Accession entries in the database that may match the names in your file due to variations in spelling and/or punctuation.
You will then be able choose which potential matches are real and those matches will be replaced automatically in your upload file.
If you'd like to manually search for existing Accession entries:
Each Accession (germplasm line) that is observed in a phenotype trial must have its own entry in the database. In addition,
the line names used in your trial design must match the names (or synonyms) of the Accessions in the database.
Use the BrAPI Germplasm Search tool
to find matches of existing Accessions (or variations in spelling and/or punctuation) for all of the lines in your trial.
If one or more of your Accessions don't exist in the database, you can add them by uploading a file of
Accession information
A Trial (a single location & year environment) must exist in the database before Trait Observations
can be added. When a Trial is created, the folllowing information is added to the database:
A phenotyping trial must exist in the database before the results can be added. The Trial contains information about
its location, plot and field size, design type, planting/harvest dates, and plot layout. For trial mean data,
create a Trial with one rep of Plots (one Plot for each Accession). Then, add the trial means as the trait value for each of the plots.
Trials and Plots must all have unique names in the database. T3/Wheat uses the following naming conventions
for Trials and Plots:
Naming Convention
Examples
Trials
In order to create a globally unique name, it is best to include a Breeding Program-specific prefix and/or experiment code,
the year of the trial, and the name of the Location.
UMOPN_2020_Urbana UIL_AYT_2020_Urbana
Plots
In order to create a globally unique name, we use the plot naming convention: {TRIAL_NAME}-PLOT{PLOT#}
UMOPN_2020_Urbana-PLOT1 UIL_AYT_2020_Urbana-PLOT1
A Trial can be added in multiple ways:
Option A - Using the trial design wizard: This will design a plot layout for you given lists
of Accessions used as entries and controls, a trial design type, and layout parameters. To design
a new trial:
Make sure you have the Accessions used as entries (and optionally as controls) in a List
Click the Design New Trial button in the top-right corner
Fill out the Trial metadata form
Select the lists of Accessions for entries and optionally checks
Select the plot layout parameters
Review the generated plot layout
Save the Trial and its plot layout to the database
View the Trial
Design manual page for more information on adding a trial using the trial design wizard.
View the Working with Lists
manual page for more information on creating and managing lists
Option B - Uploading a plot layout spreadsheet for a single trial: This option can be used if
you've already generated the plot layout and you can create a spreadsheet describing the plot layout for the trial.
To upload an existing trial design:
Click the Upload Existing Trial(s) button in the top-right corner
On Step 2, select the Single Trial Design tab
Create an Excel (.xls) file (Download blank template) that describes the plot layout with the specified headers
(Click Single trial spreadsheet for more information). The following columns
are required:
plot_name - must be unique across the database (ie: UEOPN_Urbana_2019-plot1)
accession_name - must match an existing Accession
plot_number - must be unique within this trial
block_number
If you have private data included in your trial, you can add a 1 to the is_private column for plots to exclude from the database.
Fill out the Trial metadata form
Upload the plot layout template
Review any possible errors in the trial and/or its design
Save the Trial and its plot layout to the database
View the Trial
Upload manual page for more information on uploading a trial design file.
Option C - Uploading a plot layout spreadhseet for multiple trials: This option can be used
for uploading multiple trials at a time by generating a spreadsheet containing the trial metadata and plot layout
information. This option does not require filling out the trial metadata form for each trial. To upload multiple
existing trial designs:
Click the Upload Existing Trial(s) button in the top-right corner
On Step 2, select the Multiple Trial Designs tab
Create an Excel (.xls) file (Download blank template) that includes the trial metadata and plot layout for each trial with the
specified headers (Click Multiple trial spreadsheet for more information, including required
columns and the data required for each column). If you have private data included in your trial, you can add a 1 to the is_private column for plots to exclude from the database.
Upload the trial design template
Review any possible errors in the trials and/or their design
Save the Trials and their plot layouts to the database
Trait Observations
Once the Trial(s) have been added to the database, Trait Observations can be added
to the Plots within the Trial(s).
To add Trait Observations, you will need:
The Plot Name (used when creating the Trial)
The Trait Name of each observation (from the Search > Traits page)
The Trait ID of each observation (from the Search > Traits page)
It is important to note the units/scale used by the trait in the database. If your observations
were recorded using a different scale, you will need to convert them to the scale used by the database first.
File Format:
The first column has the header observationunit_name and contains the Plot Name (or Subplot Name or Plant Name, but it is almost always going to be the Plot Name)
Add an additional column for each trait being stored. The column header follows the format {Trait Name}|{Trait ID}
and contains the trait values for each Plot. Unobserved plots should be left blank.
Once a Trial has been created, phenotype observations can be added to the Trial. If you use the
Field Book tablet app, you can create a file for
recording your observations directly on Field Book. If you already have data, you can download a spreadsheet
template specifically for the trial.
View the Working with Lists
manual page for more information on creating and managing lists
If you are familiar with the traits on the original version of T3/Wheat, you can use the trait lookup table to match
the old trait names to their corresponding Breedbase trait names and IDs. There is a trait lookup table available for each crop:
If you've forgotten your username, enter your email address below. An email will be sent with any account username(s) associated with your email address.
Reset Password
To reset your password, please enter your email address. A link will be sent to that address with a link that will enable you to reset your password.
Download Templates
Download Templates
